why equilibration step is required before md simulation

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Equilibration is an essential step before performing molecular dynamics (MD) simulations. In this step, the system is allowed to reach a stable and balanced state, or equilibrium, by adjusting its temperature, pressure, and other thermodynamic parameters to their desired values. Equilibration is necessary because MD simulations require an initial configuration of the system, and the starting configuration can significantly affect the outcome of the simulation.


During equilibration, the system is typically subjected to a series of energy minimization and molecular dynamics simulations, with the parameters gradually adjusted to reach the desired equilibrium state. This process helps to remove any unphysical contacts or stresses in the system and ensures that the initial configuration is representative of the system's true equilibrium state.


Equilibration is necessary because MD simulations are based on solving the equations of motion of the atoms or molecules in the system. These equations describe the positions and velocities of the atoms or molecules, and the forces acting on them due to interatomic or intermolecular interactions. If the system is not at equilibrium, these equations may not accurately represent the true behavior of the system, leading to inaccurate simulation results.


In summary, equilibration is required before MD simulations to ensure that the initial configuration of the system is representative of its true equilibrium state and to allow the system to reach a stable and balanced state. This step is critical for obtaining accurate and meaningful results from MD simulations

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